PDB entry 6vzh

View 6vzh on RCSB PDB site
Description: Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311
Class: transferase/transferase inhibitor
Keywords: protein kinase, inhibitor, Structural Genomics, Structural Genomics Consortium, SGC, TRANSFERASE-TRANSFERASE INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR complex
Deposited on 2020-02-28, released 2020-03-11
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-03-11, with a file datestamp of 2020-03-06.
Experiment type: XRAY
Resolution: 2.55 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.08: d6vzha_
  • Chain 'B':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.08: d6vzhb_
  • Chain 'C':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.08: d6vzhc_
  • Chain 'D':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.08: d6vzhd_
  • Heterogens: RYA, SO4, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6vzhA (A:)
smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
eiee

    Sequence, based on observed residues (ATOM records): (download) 
    >6vzhA (A:)
aeqfavgeiitdmaaaawkvglpigciyladmnssesvgsdapcvvkvepsdngplftel
kfyqraakpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyea
nakrfsrktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayry
cpegvhkayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwedn
lkdpkyvrdskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdil
lqglkaigskddgkldl

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6vzhB (B:)
smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
eiee

    Sequence, based on observed residues (ATOM records): (download) 
    >6vzhB (B:)
favgeiitdmaaaawkvglpiciyladmnssdapcvvkvepgplftelkfyqraakpeqi
qkwirtrklkylgvpkywgsglhdkyrfmimdrfgsdlqkiyeanakrfsrktvlqlslr
ildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycpegvhkayaadpkrc
hdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlkdpkyvrdskiryre
niaslmdkcfpaanapgeiakymetvklldytekplyenlrdillqglkaigskddgkld
l

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6vzhC (C:)
smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
eiee

    Sequence, based on observed residues (ATOM records): (download) 
    >6vzhC (C:)
eqfavgeiitdmaaaawkvglpiciyladmnssesvgsdapcvvkvepsdngplftelkf
yqraakpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyeana
krfsrktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycp
egvhkayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlk
dpkyvrdskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdillq
glkaigskddgkldl

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6vzhD (D:)
smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
eiee

    Sequence, based on observed residues (ATOM records): (download) 
    >6vzhD (D:)
qfavgeiitdmaaaawkvglpiciyladmnsvgsdapcvvkvepsdngplftelkfyqra
akpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyeanakrfs
rktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycpegvh
kayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlkdpky
vrdskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdillqglka
igskddgkldl